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rdkit/Python/Chem/MACCSkeys.py

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# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
#
""" SMARTS definitions for the publically available MACCS keys
and a MACCS fingerprinter
"""
import Chem
import DataStructs
# these are SMARTS patterns corresponding to the MDL MACCS keys
smartsPatts={
1:('?',0), # ISOTOPE
#2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0), # ISOTOPE Not complete
2:('[#103,#104]',0), # ISOTOPE Not complete
3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...) *NOTE* spec wrong
4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide
5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...) *NOTE* spec wrong
6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide
7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong
8:('[!C;!c;!#1]1~*~*~*~1',0), # QAAA@1
9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...)
10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth)
11:('*1~*~*~*~1',0), # 4M Ring
12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
13:('[O,o]~[N,n](~[C,c])~[C,c]',0), # ON(C)C
14:('[S,s]-[S,s]',0), # S-S
15:('[O,o]~[C,c](~[O,o])~[O,o]',0), # OC(O)O
16:('[!C;!c;!#1]1~*~*~1',0), # QAA@1
17:('[C,c]#[C,c]',0), #CTC
18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong
19:('*1~*~*~*~*~*~*~1',0), # 7M Ring
20:('[Si]',0), #Si
21:('[C,c]=[C,c](~[!C;!c;!#1])~[!C;!c;!#1]',0), # C=C(Q)Q
22:('*1~*~*~1',0), # 3M Ring
23:('[N,n]~[C,c](~[O,o])~[O,o]',0), # NC(O)O
24:('[N,n]-[O,o]',0), # N-O
25:('[N,n]~[C,c](~[N,n])~[N,n]',0), # NC(N)N
26:('[C,c]=;@[C,c](@*)@*',0), # C$=C($A)$A
27:('[I]',0), # I
28:('[!C;!c;!#1]~[CH2]~[!C;!c;!#1]',0), # QCH2Q
29:('P',0),# P
30:('[C,c]~[!C;!c;!#1](~[C,c])(~[C,c])~*',0), # CQ(C)(C)A
31:('[!C;!c;!#1]~[F,Cl,Br,I]',0), # QX
32:('[C,c]~[S,s]~[N,n]',0), # CSN
33:('[N,n]~[S,s]',0), # NS
34:('[CH2]=*',0), # CH2=A
35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
36:('[$(S@*),$(s@*)]',0), # S Heterocycle
37:('[N,n]~[C,c](~[O,o])~[N,n]',0), # NC(O)N
38:('[N,n]~[C,c](~[C,c])~[N,n]',0), # NC(C)N
39:('[O,o]~[S,s](~[O,o])~[O,o]',0), # OS(O)O
40:('[S,s]-[O,o]',0), # S-O
41:('[C,c]#[N,n]',0), # CTN
42:('F',0), # F
43:('[!C;!c;!#1;H,H2,H3,H4]~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAQH FIX: possibly incomplete
44:('?',0), # OTHER
45:('[C,c]=[C,c]~[N,n]',0), # C=CN
46:('Br',0), # BR
47:('[S,s]~*~[N,n]',0), # SAN
48:('[O,o]~[!C;!c;!#1](~[O,o])(~[O,o])~*',0), # OQ(O)O
49:('[-,-2,-3,-4,+,+2,+3,+4]',0), # CHARGE FIX: possibly incomplete
50:('[C,c]=[C,c](~[C,c])~[C,c]',0), # C=C(C)C
51:('[C,c]~[S,s]~[O,o]',0), # CSO
52:('[N,n]~[N,n]',0), # NN
53:('[!C;!c;!#1;H,H2,H3,H4]~*~*~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAAAQH FIX: possibly incomplete
54:('[!C;!c;!#1;H,H2,H3,H4]~*~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAAQH FIX: possibly incomplete
55:('[O,o]~[S,s]~[O,o]',0), #OSO
56:('[O,o]~[N,n](~[O,o])~[C,c]',0), # ON(O)C
57:('[$(O@*),$(o@*)]',0), # O Heterocycle
58:('[!C;!c;!#1]~[S,s]~[!C;!c;!#1]',0), # QSQ
59:('[S,s]!:*:*',0), # Snot%A%A
60:('[S,s]=[O,o]',0), # S=O
61:('*~[S,s](~*)~*',0), # AS(A)A
62:('*@*!@*@*',0), # A$!A$A
63:('[N,n]=[O,o]',0), # N=O
64:('*@*!@[S,s]',0), # A$A!S
65:('[C,c]:[N,n]',0), # C%N
66:('[C,c]~[C,c](~[C,c])(~[C,c])~*',0), # CC(C)(C)A
67:('[!C;!c;!#1]~[S,s]',0), # QS
68:('[!C;!c;!#1;H,H2,H3,H4]~[!C;!c;!#1;H,H2,H3,H4]',0), # QHQH FIX: possibly incomplete
69:('[!C;!c;!#1]~[!C;!c;!#1;H,H2,H3,H4]',0), # QQH FIX: possibly incomplete
70:('[!C;!c;!#1]~[N,n]~[!C;!c;!#1]',0), # QNQ
71:('[N,n]~[O,o]',0), # NO
72:('[O,o]~*~*~[O,o]',0), # OAAO
73:('[S,s]=*',0), # S=A
74:('[CH3]~*~[CH3]',0), # CH3ACH3
75:('*!@[N,n]@*',0), # A!N$A
76:('[C,c]=[C,c](~*)~*',0), # C=C(A)A
77:('[N,n]~*~[N,n]',0), # NAN
78:('[C,c]=[N,n]',0), # C=N
79:('[N,n]~*~*~[N,n]',0), # NAAN
80:('[N,n]~*~*~*~[N,n]',0), # NAAAN
81:('[S,s]~*(~*)~*',0), # SA(A)A
82:('*~[CH2]~[!C;!c;!#1;H,H2,H3,H4]',0), # ACH2QH
83:('[!C;!c;!#1]1~*~*~*~*~1',0), # QAAAA@1
84:('[NH2]',0), #NH2
85:('[C,c]~[N,n](~[C,c])~[C,c]',0), # CN(C)C
86:('[CH2][!C;!c;!#1][CH2]',0), # CH2QCH2
87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
88:('[S,s]',0), # S
89:('[O,o]~*~*~*~[O,o]',0), # OAAAO
90:('[!C;!c;!#1;H,H2,H3,H4]~*~*~[CH2]~*',0), # QHAACH2A
91:('[!C;!c;!#1;H,H2,H3,H4]~*~*~*~[CH2]~*',0), # QHAAACH2A
92:('[O,o]~[C,c](~[N,n])~[C,c]',0), # OC(N)C
93:('[!C;!c;!#1]~[CH3]',0), # QCH3
94:('[!C;!c;!#1]~[N,n]',0), # QN
95:('[N,n]~*~*~[O,o]',0), # NAAO
96:('*1~*~*~*~*~1',0), # 5 M ring
97:('[N,n]~*~*~*~[O,o]',0), # NAAAO
98:('[!C;!c;!#1]1~*~*~*~*~*~1',0), # QAAAAA@1
99:('[C,c]=[C,c]',0), # C=C
100:('*~[CH2]~[N,n]',0), # ACH2N
101:('[r8,r9,r10,r11,r12]',0), # 8M Ring or larger FIX: This is not exhaustive and it appears that oelib doesn't do this right
102:('[!C;!c;!#1]~[O,o]',0), # QO
103:('Cl',0), # CL
104:('[!C;!c;!#1;H,H2,H3,H4]~*~[CH2]~*',0), # QHACH2A
105:('[!C;!c;!#1]@*(@*)@*',0), # A$A($A)$A
106:('[!C;!c;!#1]~*(~[!C;!c;!#1])~[!C;!c;!#1]',0), # QA(Q)Q
107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
109:('*~[CH2]~[O,o]',0), # ACH2O
110:('[N,n]~[C,c]~[O,o]',0), # NCO
111:('[N,n]~*~[CH2]~*',0), # NACH2A
112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
113:('[O,o]!:*:*',0), # Onot%A%A
114:('[CH3]~[CH2]~*',0), # CH3CH2A
115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
116:('[CH3]~*~*~[CH2]~*',0), # CH3AACH2A
117:('[N,n]~*~[O,o]',0), # NAO
118:('*~[CH2]~[CH2]~*',1), # ACH2CH2A > 1
119:('[N,n]=*',0), # N=A
120:('[!C;!c;R]',1), # Heterocyclic atom > 1
121:('[$(N@*),$(n@*)]',0), # N Heterocycle
122:('*~[N,n](~*)~*',0), # AN(A)A
123:('[O,o]~[C,c]~[O,o]',0), # OCO
124:('[!C;!c;!#1]~[!C;!c;!#1]',0), # QQ
125:('?',0), # Aromatic Ring > 1
126:('*!@[O,o]!@*',0), # A!O!A
127:('*@*!@[O,o]',1), # A$A!O > 1
128:('*~[CH2]~*~*~*~[CH2]~*',0), # ACH2AAACH2A
129:('*~[CH2]~*~*~[CH2]~*',0), # ACH2AACH2A
130:('[!C;!c;!#1]~[!C;!c;!#1]',1), # QQ > 1 (&...)
131:('[!C;!c;!#1;H,H2,H3,H4]',1), # QH > 1
132:('[O,o]~*~[CH2]~*',0), # OACH2A
133:('*@*!:[N,n]',0), # A$A!N
134:('[F,Cl,Br,I]',0), # X (HALOGEN)
135:('[N,n]!:*:*',0), # Nnot%A%A
136:('[O,o]=*',1), # O=A>1 FIX: maybe not right key
137:('[!C;!c;R]',0), # Heterocycle
138:('[!C;!c;!#1]~[CH2]~*',1), # QCH2A>1 (&...)
139:('[OH,OH2,OH3]',0), # OH
140:('[O,o]',3), # O > 3
141:('[CH3]',2), # CH3 > 2
142:('[N,n]',1), # N > 1
143:('*@*!@[O,o]',0), # A$A!O
144:('*!:*:*!:*',0), # Anot%A%Anot%A
145:('*1~*~*~*~*~*~1',1), # 6M ring > 1
146:('[O,o]',2), # O > 2
147:('*~[CH2]~[CH2]~*',0), # ACH2CH2A
148:('*~[!C;!c;!#1](~*)~*',0), # AQ(A)A
149:('[CH3]',1), # CH3 > 1
150:('*!@*@*!@*',0), # A!A$A!A
151:('[NH,NH2,NH3,NH4]',0), # NH
152:('[O,o]~[C,c](~[C,c])~[C,c]',0), # OC(C)C
153:('[!C;!c;!#1]~[CH2]~*',0), # QCH2A
154:('[C,c]=[O,o]',0), # C=O
155:('*!@[CH2]!@*',0), # A!CH2!A
156:('[N,n]~*(~*)~*',0), # NA(A)A
157:('[C,c]-[O,o]',0), # C-O
158:('[C,c]-[N,n]',0), # C-N
159:('[O,o]',1), # O>1
160:('[CH3]',0), #CH3
161:('[N,n]',0), # N
162:('a',0), # Aromatic
163:('*1~*~*~*~*~*~1',0), # 6M Ring
164:('[O,o]',0), # O
165:('[R]',0), # Ring
166:('?',0), # Fragments FIX: this should be (*).(*), but that doesn't work properly in oelib
}
maccsKeys = None
def _InitKeys(keyList,keyDict):
""" *Internal Use Only*
generates SMARTS patterns for the keys, run once
"""
assert len(keyList) == len(keyDict.keys()),'length mismatch'
for key in keyDict.keys():
patt,count = keyDict[key]
if patt != '?':
try:
sma = Chem.MolFromSmarts(patt)
except:
sma = None
if not sma:
print 'SMARTS parser error for key #%d: %s'%(key,patt)
else:
keyList[key-1] = sma,count
def GenMACCSKeys(mol,**kwargs):
""" generates the MACCS fingerprint for a molecules
**Arguments**
- mol: the molecule to be fingerprinted
- any extra keyword arguments are ignored
**Returns**
a _DataStructs.SparseBitVect_ containing the fingerprint.
>>> m = Chem.MolFromSmiles('CNO')
>>> bv = GenMACCSKeys(m)
>>> tuple(bv.GetOnBits())
(24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164)
>>> bv = GenMACCSKeys(Chem.MolFromSmiles('CCC'))
>>> tuple(bv.GetOnBits())
(74, 114, 149, 155, 160)
"""
global maccsKeys
if maccsKeys is None:
maccsKeys = [(None,0)]*len(smartsPatts.keys())
_InitKeys(maccsKeys,smartsPatts)
res = DataStructs.SparseBitVect(len(maccsKeys)+1)
for i,(patt,count) in enumerate(maccsKeys):
if patt is not None:
matches = mol.GetSubstructMatches(patt)
if matches:
if count == 0:
res[i+1] = 1
else:
if len(matches) > count:
res[i+1] = 1
return res
FingerprintMol = GenMACCSKeys
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"])
if __name__ == '__main__':
import sys
failed,tried = _test()
sys.exit(failed)
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